diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..3d47f986c41db29ec6dc0d5036bf760b3a1cf366
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+.idea/
+target/
+.settings/
+*.iml
+.project
+.classpath
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b8ffa4f9cc71d9646a8e0ed9a2e1ce07cbc9c756
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,89 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.3</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>image-to-workbook</artifactId>
+ <version>2.5.3</version>
+
+ <packaging>jar</packaging>
+
+ <name>Image to Workbook</name>
+ <description>Convert a 2D Image to workbook</description>
+ <url>http://icy.bioimageanalysis.org/plugin/image-to-workbook/</url>
+ <inceptionYear>2020</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>sdallongeville</id>
+ <name>Stéphane Dallongeville</name>
+ <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url>
+ <roles>
+ <role>founder</role>
+ <role>lead</role>
+ <role>architect</role>
+ <role>developer</role>
+ <role>debugger</role>
+ <role>tester</role>
+ <role>maintainer</role>
+ <role>support</role>
+ </roles>
+ </developer>
+ </developers>
+
+ <!-- Project properties -->
+ <properties>
+
+ </properties>
+
+ <!-- Project build configuration -->
+ <build>
+
+ </build>
+
+ <!-- List of project's dependencies -->
+ <dependencies>
+ <!-- The core of Icy -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>workbooks</artifactId>
+ <version>3.4.10</version>
+ </dependency>
+ </dependencies>
+
+ <!-- Icy Maven repository (to find parent POM) -->
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <name>Icy's Nexus</name>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/worm/image2workbook/Image2Workbook.java b/src/main/java/plugins/worm/image2workbook/Image2Workbook.java
new file mode 100644
index 0000000000000000000000000000000000000000..0585b378844070f3b0d6b2f5ef7f107e9e0960d9
--- /dev/null
+++ b/src/main/java/plugins/worm/image2workbook/Image2Workbook.java
@@ -0,0 +1,464 @@
+package plugins.worm.image2workbook;
+
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GradientPaint;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.BufferedWriter;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.HashMap;
+
+import javax.swing.JComponent;
+import javax.swing.JLayeredPane;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.jdesktop.swingx.JXButton;
+
+import icy.canvas.IcyCanvas;
+import icy.file.FileUtil;
+import icy.gui.dialog.MessageDialog;
+import icy.gui.dialog.SaveDialog;
+import icy.gui.frame.IcyFrame;
+import icy.gui.frame.progress.ToolTipFrame;
+import icy.gui.viewer.Viewer;
+import icy.gui.viewer.ViewerEvent;
+import icy.gui.viewer.ViewerEvent.ViewerEventType;
+import icy.gui.viewer.ViewerListener;
+import icy.image.IcyBufferedImage;
+import icy.painter.Overlay;
+import icy.plugin.abstract_.PluginActionable;
+import icy.sequence.Sequence;
+import icy.sequence.SequenceEvent;
+import icy.sequence.SequenceListener;
+import icy.system.IcyHandledException;
+import icy.type.point.Point5D;
+import plugins.adufour.vars.gui.swing.WorkbookEditor;
+import plugins.adufour.vars.lang.VarWorkbook;
+
+public class Image2Workbook extends PluginActionable
+{
+ public static final HashMap<Viewer, MagnifierOverlay> magnifiers = new HashMap<Viewer, Image2Workbook.MagnifierOverlay>();
+ // squence chooser define
+ // SequenceChooser sq = new SequenceChooser( true, "Input Sequence");
+ Sequence sequence;
+ // workbook define
+ VarWorkbook wb = new VarWorkbook("workbook", "Result");
+ WorkbookEditor ed = new WorkbookEditor(wb);
+ // save button define
+ JXButton buttonSave = new JXButton("Save workbook as...");
+ IcyFrame mainFrame = new IcyFrame("Image2Workbook Result");
+
+ @Override
+ public void run()
+ {
+ Viewer viewer = getActiveViewer();
+
+ if (viewer == null)
+ throw new IcyHandledException("Open an image before using the magnifier");
+
+ if (magnifiers.containsKey(viewer))
+ return;
+
+ if (viewer.getSequence() == null)
+ throw new IcyHandledException("The active viewer contains no sequence");
+
+ magnifiers.put(viewer, new MagnifierOverlay(viewer, viewer.getSequence().getSizeC() - 1, 4, wb, mainFrame));
+
+ ed.setEnabled(true);
+ // sq.setActiveSequenceSelected();
+ // main editor
+
+ mainFrame.setResizable(true);
+ mainFrame.setLayout(new BorderLayout());
+ // north panel
+ // JXPanel NorthPanel = new JXPanel();
+ // //sq.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e) {
+ // sequence = sq.getSelectedSequence();
+ // //ImageToWorkbook(sequence,wb);
+ // }
+ // });
+
+ // NorthPanel.add(sq);
+ // South panel
+ // JXPanel SouthPanel = new JXPanel();
+ // buttonSave.addActionListener(new ActionListener()
+ // {
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // String path = SaveDialog.chooseFile("Save workbook as...", null, "Workbook", ".xls");
+ // if (path == null) return;
+ //
+ // try
+ // {
+ // FileOutputStream fos = new FileOutputStream(path);
+ // wb.getValue().write(fos);
+ // fos.close();
+ // }
+ // catch (IOException e1)
+ // {
+ // MessageDialog.showDialog(e1.getMessage(), MessageDialog.ERROR_MESSAGE);
+ // }
+ // }
+ //
+ //
+ // });
+ // SouthPanel.add(buttonSave);
+ // show the workbook
+ JComponent cp = ed.getEditorComponent();
+ cp.setPreferredSize(new Dimension(600, 600));
+ mainFrame.add(cp, BorderLayout.CENTER);
+ // show the button and squencechooser
+ // mainFrame.add(NorthPanel, BorderLayout.NORTH);
+ // mainFrame.add(SouthPanel,BorderLayout.NORTH);
+ // Pack and show the window
+ mainFrame.pack();
+ mainFrame.addToDesktopPane(JLayeredPane.DEFAULT_LAYER);
+ mainFrame.setVisible(true);
+
+ // }
+ }
+
+ private static final class MagnifierOverlay extends Overlay implements SequenceListener, ViewerListener
+ {
+ private final Sequence sequence;
+ private final ToolTipFrame frame = new ToolTipFrame(
+ "<b>Image2Workbook instructions:</b><br/><ul><li>Press 'c' to toggle between channels</li>"
+ + "<li>Press 'a' to save the sequence data</li>"
+ + "<li>Press 's' to save current image data</li>" + "<li>Press 'q' to close</li>"
+ + "<li>Press 'space' to toggle the workbook refresh mode</li></ul>");
+
+ float currentPosX, currentPosY;
+ int currentChannel = 0;
+
+ private int scale;
+ AffineTransform xForm = new AffineTransform();
+
+ int radius = 50;
+ int diameter = radius * 2;
+ GradientPaint paintBlack = new GradientPaint(0, 0, Color.black, radius, radius, Color.darkGray.darker(), true);
+ GradientPaint paintGreen = new GradientPaint(0, 0, Color.green, radius, radius, Color.lightGray.darker(), true);
+
+ Rectangle2D.Float lens = new Rectangle2D.Float();
+ final Viewer viewer;
+ Boolean RefreshWorkbookMode = true;
+ VarWorkbook wb;
+ IcyFrame mainFrame;
+
+ public MagnifierOverlay(Viewer viewer, int initialChannel, int magnifierScale, VarWorkbook w, IcyFrame frame)
+ {
+ super("Magnifier");
+ wb = w;
+ mainFrame = frame;
+ this.viewer = viewer;
+ this.sequence = viewer.getSequence();
+ this.currentChannel = initialChannel;
+ sequence.addOverlay(this);
+ radius = Math.min(Math.min(sequence.getSizeX() / 2, sequence.getSizeY()) / 2, 50);
+ diameter = radius * 2;
+ paintBlack = new GradientPaint(0, 0, Color.black, radius, radius, Color.darkGray.darker(), true);
+ paintGreen = new GradientPaint(0, 0, Color.green, radius, radius, Color.lightGray.darker(), true);
+
+ sequence.addListener(this);
+ viewer.addListener(this);
+ setScale(magnifierScale);
+ }
+
+ private void setScale(int scale)
+ {
+ this.scale = scale;
+ new Font("Tahoma", Font.PLAIN, scale).deriveFont(scale * 0.1f);
+ }
+
+ private void updateImageCache()
+ {
+
+ currentChannel = Math.min(currentChannel, sequence.getSizeC());
+
+ }
+
+ @Override
+ public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
+ {
+ // don't paint on other viewers
+ if (viewer.getCanvas() != canvas)
+ return;
+ boolean displayValues = RefreshWorkbookMode;// currentZoom >= 2f;
+
+ float xo = currentPosX - radius;
+ float yo = currentPosY - radius;
+
+ // canvas.getScaleX();
+
+ // draw the lens
+ Graphics2D graphics = (Graphics2D) g.create();
+ graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED);
+
+ if (displayValues)
+ graphics.setPaint(paintGreen);
+ else
+ graphics.setPaint(paintBlack);
+
+ if (radius >= 5)
+ graphics.setStroke(new BasicStroke((float) 1));
+ else
+ graphics.setStroke(new BasicStroke((float) 0.1));
+
+ graphics.draw(lens);
+
+ // draw the "zoomed" image inside the lens
+ graphics.clip(lens);
+ // graphics.translate(xForm.getTranslateX(), xForm.getTranslateY());
+ // graphics.scale(scale, scale);
+ // canvas.getImageLayer().getOverlay().paint(graphics, sequence, canvas);
+
+ graphics.dispose();
+ // draw pixel values
+
+ if (displayValues)
+ {
+ IcyBufferedImage im = canvas.getCurrentImage();
+ Sheet sheet = wb.getValue().getSheetAt(0);
+
+ // int k=0;c
+ for (int j = (int) yo; j < yo + diameter; j++)
+ {
+ Row row = sheet.createRow((int) (j - yo));
+
+ // int m=0;
+ for (int i = (int) xo; i < xo + diameter; i++)
+ {
+ Cell cell = row.createCell((int) (i - xo));
+
+ if (im.getBounds().contains(i, j))
+ cell.setCellValue(im.getData(i, j, currentChannel));
+ else
+ cell.setCellValue(0);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void mouseMove(MouseEvent e, Point5D.Double imagePoint, IcyCanvas canvas)
+ {
+ boolean displayValues = RefreshWorkbookMode;
+ if (!displayValues)
+ return;
+ currentPosX = (float) imagePoint.getX();
+ currentPosY = (float) imagePoint.getY();
+
+ if (currentPosX < radius)
+ currentPosX = radius;
+ if (currentPosY < radius)
+ currentPosY = radius;
+ if (currentPosX > (viewer.getSequence().getSizeX() + radius))
+ currentPosX = viewer.getSequence().getSizeX() + radius;
+ if (currentPosY > (viewer.getSequence().getSizeY() + radius))
+ currentPosY = viewer.getSequence().getSizeY() + radius;
+ radius = Math.min(Math.min(sequence.getSizeX() / 2, sequence.getSizeY() / 2), 50);
+ diameter = radius * 2;
+ paintBlack = new GradientPaint(0, 0, Color.black, radius, radius, Color.darkGray.darker(), true);
+ paintGreen = new GradientPaint(0, 0, Color.green, radius, radius, Color.lightGray.darker(), true);
+
+ xForm.setToTranslation(-currentPosX * scale + currentPosX, -currentPosY * scale + currentPosY);
+ lens.setFrame(currentPosX - radius, currentPosY - radius, diameter, diameter);
+
+ mainFrame.setTitle(sequence.getName() + " @Channel " + new Integer(currentChannel).toString()
+ + " Location @ " + '(' + new Double(Math.round((double) (currentPosX - radius))).toString() + " "
+ + ',' + " " + new Double(Math.round((double) (currentPosY - radius))).toString() + ')');
+ canvas.repaint();
+ mainFrame.repaint();
+
+ super.mouseMove(e, imagePoint, canvas);
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+ if (canvas.getViewer() != viewer)
+ return;
+
+ if ((e.getKeyChar() == 'c') || (e.getKeyChar() == 'C'))
+ {
+ currentChannel = (currentChannel + 1) % (canvas.getCurrentImage().getSizeC());
+ mainFrame.setTitle(sequence.getName() + " @Channel " + new Integer(currentChannel).toString()
+ + " Location @ " + '(' + new Double(Math.round((double) (currentPosX - radius))).toString()
+ + " " + ',' + " " + new Double(Math.round((double) (currentPosY - radius))).toString() + ')');
+ canvas.repaint();
+ mainFrame.repaint();
+ }
+ else if ((e.getKeyChar() == 's') || (e.getKeyChar() == 'S'))
+ {
+ saveWorkbook();
+ }
+ else if ((e.getKeyChar() == 'a') || (e.getKeyChar() == 'A'))
+ {
+ saveAllData(sequence);
+ }
+ else if ((e.getKeyChar() == 'q') || (e.getKeyChar() == 'Q'))
+ {
+ mainFrame.close();
+ remove();
+ }
+ else if (e.getKeyCode() == KeyEvent.VK_SPACE)
+ {
+ RefreshWorkbookMode = !RefreshWorkbookMode;
+ }
+ }
+
+ @Override
+ public void remove()
+ {
+ frame.close();
+ super.remove();
+ if (sequence != null)
+ sequence.removeListener(this);
+ if (viewer != null)
+ viewer.removeListener(this);
+ magnifiers.remove(viewer);
+ }
+
+ @Override
+ public void sequenceChanged(SequenceEvent sequenceEvent)
+ {
+ switch (sequenceEvent.getSourceType())
+ {
+ case SEQUENCE_DATA:
+ case SEQUENCE_COLORMAP:
+
+ updateImageCache();
+
+ default:
+ break;
+ }
+ }
+
+ @Override
+ public void sequenceClosed(Sequence sequence)
+ {
+ remove();
+ }
+
+ @Override
+ public void viewerChanged(ViewerEvent event)
+ {
+ if (event.getType() == ViewerEventType.CANVAS_CHANGED)
+ remove();
+ }
+
+ @Override
+ public void viewerClosed(Viewer viewer)
+ {
+ remove();
+ }
+
+ public void saveWorkbook()
+ {
+ String path = SaveDialog.chooseFile("Save workbook as...", null, "Workbook", ".xls");
+ if (path == null)
+ return;
+
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(path);
+ wb.getValue().write(fos);
+ fos.close();
+ }
+ catch (IOException e1)
+ {
+ MessageDialog.showDialog(e1.getMessage(), MessageDialog.ERROR_MESSAGE);
+ }
+ }
+
+ public void saveImageData(String path, Sequence sequence, int t, int z)
+ {
+
+ if (path == null)
+ return;
+ if (!(path.contains(".csv")))
+ {
+ path = path.concat(".csv");
+ }
+ for (int channel = 0; channel < sequence.getSizeC(); channel++)
+ {
+ IcyBufferedImage im = sequence.getImage(t, z, channel);
+
+ try
+ {
+ FileWriter fw = new FileWriter(
+ path.replace(".csv", '_' + "channel" + new Integer(channel).toString() + ".csv"), false);
+
+ BufferedWriter bw = new BufferedWriter(fw);
+ for (int y = 0; y < im.getSizeY(); y++)
+ {
+
+ for (int x = 0; x < im.getSizeX() - 1; x++)
+ {
+ bw.write(new Double(im.getData(x, y, 0)).toString());
+ bw.write(',');
+ }
+ bw.write(new Double(im.getData(im.getSizeX() - 1, y, 0)).toString());
+ bw.write('\n');
+ bw.flush();
+ }
+ bw.close();
+ fw.close();
+ }
+ catch (IOException e1)
+ {
+ MessageDialog.showDialog(e1.getMessage(), MessageDialog.ERROR_MESSAGE);
+ }
+ }
+
+ }
+
+ public void saveAllData(Sequence sequence)
+ {
+ String pathchanged;
+
+ String path = SaveDialog.chooseFile("Save current image as...", null,
+ sequence.getName().toString() + ".csv");
+ if (path == null)
+ return;
+ path = path.replace(".csv", "").replace(".CSV", "");
+
+ FileUtil.createDir(path);
+ path = path + '/' + sequence.getName().toString();
+ for (int T = 0; T < sequence.getSizeT(); T++)
+ {
+ for (int Z = 0; Z < sequence.getSizeZ(); Z++)
+ {
+
+ if (!(path.contains(".csv")))
+ {
+ path = path.concat(".csv");
+ }
+
+ pathchanged = path.replace(".csv",
+ '_' + "t" + new Integer(T).toString() + '_' + "z" + new Integer(Z).toString() + ".csv");
+ saveImageData(pathchanged, sequence, T, Z);
+
+ }
+ }
+ }
+
+ }
+}